So the thing of it being dangerous to deny that the existence of God could be proven by reason may have been a more 17th/18th century phenomenon. As intellectuals got less religious, that made it possible to fear that someone like Pierre Bayle was secretly an atheist (and actually, historians still aren't sure what to make of Bayle). That was probably less of an issue in the middle ages.
That said, the Summa is a rather blatant example of writing down your bottom line first and then going back and figuring out how to argue for it. Aquinas is constantly noting how some point of Aristotle's views may seem to conflict with Christianity, but every single time it miraculously turns out that Aristotle has been misunderstood and his views don't actually conflict with Christianity (there might be one or two exceptions to this where Aquinas is forced to conclude Aristotle was wrong about something, but if there are they're very rare, and I'm not actually sure there are any at all).
This was in the context of a fair number of people in Aquinas' time reading their Aristotle (and Averroes) and actually drawing the heretical conclusions. It's not clear to me whether the "doctrine of double truth" was something anyone actually advocated, but assuming it was it appears to have been a dodge to allow heretical Aristotelians to advocate their heretical ideas while saying, "oh, this is just the conclusions you can reach by reason, we also recognize there are contrary conclusions that can be reached by faith."
(Actually, come to think of it, this is pretty much Bayle's strategy centuries later. The big difference is the focus on heresy vs. focus on atheism.)
In other words, the people who were targets for the inquisition were the people who were saying heretical truths could be discovered by reason. If you said the orthodox view could be discovered by reason, church authorities weren't going to haul you before the inquisition because your arguments for the orthodox view weren't strong enough.
People who take for granted that Aquinas was a great philosopher because everyone says so need to stop and consider how the history of medieval philosophy might have turned out differently if the more heretical strains of Aristotelianism hadn't been suppressed.
Continuing my quest to untangle people's confusions about Eliezer's metaethics... I've started to wonder if maybe some people have the intuition that the orthogonality thesis is at odds with moral realism.
I personally have a very hard time seeing why anyone would think that, perhaps in part because of my experience in philosophy of religion. Theistic apologists would love to be able to say, "moral realism, therefore a sufficiently intelligent being would also be good." It would help patch some obvious holes in their arguments and help them respond to things like Stephen Law's Evil God Challenge. But they mostly don't even try to argue that, for whatever reason.
You did see philosophers claiming things like that back in the bad old days before Kant, which raises the question of what's changed. I suspect the reason is fairly mundane, though: before Kant (roughly), it was not only dangerous to be an atheist, it was dangerous to question that the existence of God could be proven through reason (because it would get you suspected of being an atheist). It was even dangerous to advocated philosophical views that might possibly undermine the standard arguments for the existence of God. That guaranteed that philosophers could used whatever half-baked premises they wanted in constructing arguments for the existence of God, and have little fear of being contradicted.
Besides, even if you think an all-knowing would also necessarily be perfectly good, it still seems perfectly possible to have an otherwise all-knowing being with a horrible blind spot regarding morality.
On the other hand, in the comments of a post on the orthogonality thesis, Stuart Armstrong mentions that:
This is not super-enlightening, partly because Stuart is talking about people whose views he admits he doesn't understand... but on the other hand, maybe Stuart agrees that there is some kind of conflict there, since he seems to imply that he himself rejects moral realism.
I realize I'm struggling a bit to guess what people could be thinking here, but I suspect some people are thinking it, so... anyone?